Originally the fans were singing a song that was anti-Semitic.
Man City beat Crystal Palace 5-0 on Saturday, while Romelu Lukaku scored the only goal as United won at Southampton.
Stoke, which was fielding a makeshift defense with Kurt Zouma ineligible and Ryan Shawcross and Kevin Wimmer out injured, is 15th in the table having recorded just win in its opening six games. Tottenham defeated West Ham 3-2 earlier.
However, there is still plenty of business to be done, with the January transfer window offering clubs the chance to bolster their squads mid-way through the Premier League season. "Stoke are a really good team and very strong", he told BBC Sport afterwards.
Cahill dropped, Hazard on the bench for Stoke clash
Kurt Zouma is ineligible to play against his parent club, while Ryan Shawcross and Geoff Cameron remain on the sidelines. Manchester United is right at the front of that, with the club posting a record revenue figure for the 2016/17 year.
"I think we have to be focused at what we do and not others", added the Italian. "He comes from sunny Spain, he's better than Harry Kane".
After the match Conte said: "It was a good day, a good result for us".
Conte said of the 24-year-old: "I like him because he's a complete player and also he has a lot of room to improve in every situation, tactical, physical, technical aspect, he's very committed, his behaviour is always fantastic".
Stoke stayed in the game until Morata finished them off with goals in the 77th and 82nd minutes, first dinking the ball over Butland and then tapping in to take his season's tally to six.
"I want to thank our fans".
- Taiwan Semiconductor Mfg. Co. Ltd. (ADR) (TSM) EPS Estimated At $0.55
- Analyst Research Roundup: Louisiana-Pacific Corporation (LPX), Capitol Federal Financial, Inc. (CFFN)
- Iran unveils missile that can reach Israel, carry multiple warheads
- 3 of the 4 Australian big banks drop foreign ATM fees
- North Korea earthquakes may be aftershocks of 3 September missile tests
- Amazon deepens its push into India with stake in local retailer
- No. 13 Virginia Tech blanks Monarchs
- Attractive vinyl set for Nier: Automata's soundtrack
- Kim calls Trump 'deranged' as Pyongyang hints at H-bomb
- Kim Jong Un says 'Deranged' Trump will 'pay dearly' for threat